An ancient burial containing chariots, gold artifacts and possible human sacrifices has been discovered by archaeologists in the country of Georgia, in the south Caucasus.

The burial site, which would've been intended for a chief, dates back over 4,000 years to a time archaeologists call the Early Bronze Age, said Zurab Makharadze, head of the Centre of Archaeology at the Georgian National Museum.

Archaeologists discoveredthe timber burial chamber within a 39-foot-high (12 meters) mound called a kurgan. When the archaeologists reached the chamber they found an assortment of treasures, including two chariots, each with four wooden wheels. [See Images of the Burial Chamber & Chariots]

...

The burial dates back to a time before domesticated horses appeared in the area, Makharadze said. While no animals were found buried with the chariots, he said, oxen would have pulled them.

Neanderthal dietary reconstructions have, to date, been based on indirect evidence and may underestimate the significance of plants as a food source. While zooarchaeological and stable isotope data have conveyed an image of Neanderthals as largely carnivorous, studies on dental calculus and scattered palaeobotanical evidence suggest some degree of contribution of plants to their diet. However, both views remain plausible and there is no categorical indication of an omnivorous diet. Here we present direct evidence of Neanderthal diet using faecal biomarkers, a valuable analytical tool for identifying dietary provenance. Our gas chromatography-mass spectrometry results from El Salt (Spain), a Middle Palaeolithic site dating to ca. 50,000 yr. BP, represents the oldest positive identification of human faecal matter. We show that Neanderthals, like anatomically modern humans, have a high rate of conversion of cholesterol to coprostanol related to the presence of required bacteria in their guts. Analysis of five sediment samples from different occupation floors suggests that Neanderthals predominantly consumed meat, as indicated by high coprostanol proportions, but also had significant plant intake, as shown by the presence of 5β-stigmastanol. This study highlights the applicability of the biomarker approach in Pleistocene contexts as a provider of direct palaeodietary information and supports the opportunity for further research into cholesterol metabolism throughout human evolution.

Seventeen Middle Pleistocene crania from the Sima de los Huesos site (Atapuerca, Spain) are analyzed, including seven new specimens. This sample makes it possible to thoroughly characterize a Middle Pleistocene hominin paleodeme and to address hypotheses about the origin and evolution of the Neandertals. Using a variety of techniques, the hominin-bearing layer could be reassigned to a period around 430,000 years ago. The sample shows a consistent morphological pattern with derived Neandertal features present in the face and anterior vault, many of which are related to the masticatory apparatus. This suggests that facial modification was the first step in the evolution of the Neandertal lineage, pointing to a mosaic pattern of evolution, with different anatomical and functional modules evolving at different rates.

June 15, 2014

This is important because (a) it shows evidence for the "slow" mutation rate in a species related to humans, (b) it shows that chimp and human mutation rates are equal and so using the human mutation rate in studies of divergence with chimps is justified, and (c) it is driven differently by males/females than in humans.Science 13 June 2014:
Vol. 344 no. 6189 pp. 1272-1275
DOI: 10.1126/science.344.6189.1272

Strong male bias drives germline mutation in chimpanzees

Oliver Venn

ABSTRACT

Germline mutation determines rates of molecular evolution, genetic diversity, and fitness load. In humans, the average point mutation rate is 1.2 × 10−8 per base pair per generation, with every additional year of father’s age contributing two mutations across the genome and males contributing three to four times as many mutations as females. To assess whether such patterns are shared with our closest living relatives, we sequenced the genomes of a nine-member pedigree of Western chimpanzees, Pan troglodytes verus. Our results indicate a mutation rate of 1.2 × 10−8 per base pair per generation, but a male contribution seven to eight times that of females and a paternal age effect of three mutations per year of father’s age. Thus, mutation rates and patterns differ between closely related species.

The genetics of Mexico recapitulates Native American substructure and affects biomedical traits

Andrés Moreno-Estrada

Mexico harbors great cultural and ethnic diversity, yet fine-scale patterns of human genome-wide variation from this region remain largely uncharacterized. We studied genomic variation within Mexico from over 1000 individuals representing 20 indigenous and 11 mestizo populations. We found striking genetic stratification among indigenous populations within Mexico at varying degrees of geographic isolation. Some groups were as differentiated as Europeans are from East Asians. Pre-Columbian genetic substructure is recapitulated in the indigenous ancestry of admixed mestizo individuals across the country. Furthermore, two independently phenotyped cohorts of Mexicans and Mexican Americans showed a significant association between subcontinental ancestry and lung function. Thus, accounting for fine-scale ancestry patterns is critical for medical and population genetic studies within Mexico, in Mexican-descent populations, and likely in many other populations worldwide.

June 13, 2014

The authors propose that a genetic component found in Horn of Africa populations back-migrated to Africa from Eurasia ~23 thousand years ago. I did not read this carefully yet, but it seems reasonably plausible. The migration uncovered by Pagani et al. and Pickrell et al. (~3kya) is probably not the whole story of Eurasian back-migration into Africa; that episode probably involved only Semitic speakers (it's hard to imagine any other language being carried from the Middle East at that time frame). But the Eurasian affiliation of East Africans extends well beyond Semitic speakers. In North Africa this is even clearer as the native (pre-Arab) population is definitely broadly West Eurasian and this must have come about by back-migration.

The back-migration of M1 and U6 into Africa seems to be at a similar time depth as the one proposed by these authors (post-initial UP, but pre-Neolithic). I have proposed that haplogroup E may represent an even earlier layer of Eurasian back-migration, while the signals identified by Pagani et al. and Pickrell et al. in East Africa, Pickrell et al. for Southern Africa, and the limited (but present) Neandertal ancestry in Yoruba and Pygmies documented by Pruefer et al. represent later events. The arrival of Arabs and Europeans are later events still.

For a time, there was a taboo against imagining back-migration into Africa; in a sense this was reasonable on parsimony grounds: Africans have most autosomal genetic diversity and the basal clades of mtDNA and Y-chromosomes; a model with Out-of-Africa is simpler than one with both Out-of and Into-Africa. However, we now know that pretty much all Africans have Eurasian ancestry, ranging from at least traces in theYoruba and Pygmies (to account for the Neandertal admixture) to intermediate values in East Africans, to quite a lot in North Africans.

Eurasian admixture in Africa seems to be general, variable, and to have occurred at different time scales. It's still the best hypothesis that modern humans originated in Africa initially and migrated into Eurasia. However, it is no longer clear that Africa was always the pump and never the destination of human migrations.PLoS Genet 10(6): e1004393. doi:10.1371/journal.pgen.1004393

Early Back-to-Africa Migration into the Horn of Africa

Jason A. Hodgson

Genetic studies have identified substantial non-African admixture in the Horn of Africa (HOA). In the most recent genomic studies, this non-African ancestry has been attributed to admixture with Middle Eastern populations during the last few thousand years. However, mitochondrial and Y chromosome data are suggestive of earlier episodes of admixture. To investigate this further, we generated new genome-wide SNP data for a Yemeni population sample and merged these new data with published genome-wide genetic data from the HOA and a broad selection of surrounding populations. We used multidimensional scaling and ADMIXTURE methods in an exploratory data analysis to develop hypotheses on admixture and population structure in HOA populations. These analyses suggested that there might be distinct, differentiated African and non-African ancestries in the HOA. After partitioning the SNP data into African and non-African origin chromosome segments, we found support for a distinct African (Ethiopic) ancestry and a distinct non-African (Ethio-Somali) ancestry in HOA populations. The African Ethiopic ancestry is tightly restricted to HOA populations and likely represents an autochthonous HOA population. The non-African ancestry in the HOA, which is primarily attributed to a novel Ethio-Somali inferred ancestry component, is significantly differentiated from all neighboring non-African ancestries in North Africa, the Levant, and Arabia. The Ethio-Somali ancestry is found in all admixed HOA ethnic groups, shows little inter-individual variance within these ethnic groups, is estimated to have diverged from all other non-African ancestries by at least 23 ka, and does not carry the unique Arabian lactase persistence allele that arose about 4 ka. Taking into account published mitochondrial, Y chromosome, paleoclimate, and archaeological data, we find that the time of the Ethio-Somali back-to-Africa migration is most likely pre-agricultural.

June 11, 2014

The paper includes a craniometric dataset on 10 variables in the supplementary material.

Nature Communications 5, Article number: 4094 doi:10.1038/ncomms5094

Craniometric analysis of European Upper Palaeolithic and Mesolithic samples supports discontinuity at the Last Glacial Maximum

Ciaraán Brewster et al.

The Last Glacial Maximum (LGM) represents the most significant climatic event since the emergence of anatomically modern humans (AMH). In Europe, the LGM may have played a role in changing morphological features as a result of adaptive and stochastic processes. We use craniometric data to examine morphological diversity in pre- and post-LGM specimens. Craniometric variation is assessed across four periods—pre-LGM, late glacial, Early Holocene and Middle Holocene—using a large, well-dated, data set. Our results show significant differences across the four periods, using a MANOVA on size-adjusted cranial measurements. A discriminant function analysis shows separation between pre-LGM and later groups. Analyses repeated on a subsample, controlled for time and location, yield similar results. The results are largely influenced by facial measurements and are most consistent with neutral demographic processes. These findings suggest that the LGM had a major impact on AMH populations in Europe prior to the Neolithic.

Neanderthal Origin of the Haplotypes Carrying the Functional Variant Val92Met in the MC1R in Modern Humans

Qiliang Ding et al.

Skin color is one of the most visible and important phenotypes of modern humans. Melanocyte-stimulating hormone and its receptor played an important role in regulating skin color. In this paper, we present evidence of Neanderthal introgression encompassing the melanocyte-stimulating hormone receptor gene MC1R. The haplotypes from Neanderthal introgression diverged with the Altai Neanderthal 103.3 KYA, which postdates the anatomically modern human – Neanderthal divergence. We further discovered that all of the putative Neanderthal introgressive haplotypes carry the Val92Met variant, a loss-of-function variant in MC1R that is associated with multiple dermatological traits including skin color and photoaging. Frequency of this Neanderthal introgression is low in Europeans (~5%), moderate in continental East Asians (~30%), and high in Taiwanese aborigines (60-70%). Since the putative Neanderthal introgressive haplotypes carry a loss-of-function variant that could alter the function of MC1R and is associated with multiple traits related to skin color, we speculate that the Neanderthal introgression may have played an important role in the local adaptation of Eurasians to sunlight intensity.

June 10, 2014

An interesting new (open access) paper in PNAS includes some new data from Crete, the Dodecanese, Cappadocia, and several other Greek (and a few non-Greek) populations, and proposes that the Neolithic followed an island-hopping migration into Europe. This is a study on modern populations that nicely complements the recent ancient mtDNA paper from PPNB which found an affinity to Neolithic Near Eastern populations among the modern inhabitants of Cyprus and Crete.

It is hard to imagine that there were ever any major impediments to gene flow between Anatolia and the Balkans as the Aegean islands and Hellespont are not formidable barriers to any culture with even rudimentary technology. Hopefully in the future it will become possible to look at ancient DNA from Greece and Anatolia and directly determine how the transfer of the Neolithic package into Europe took place and how much of the ancestry of modern populations stems from the Neolithic inhabitants vs. more recent shuffling of genes in either direction.

The authors also computed f3-statistics to see if populations were admixed, but found no significant evidence for it. If, for example, Dodecanesians were intermediate between mainland Greece and Anatolia they might have a negative f3(Dodecanesian; Cappadocia, Peloponnese) statistic. A negative statistic proves admixture but a positive one does not disprove it, but, in any case, there is no signal of admixture here so the results are compatible with the authors' model and probably incompatible with a recent admixture that would leave a significant negative signal (i.e., Dodecanesians/Cretans would have intermediate allele frequencies between Cappadocians and mainland Greeks).

PNAS doi: 10.1073/pnas.1320811111

Maritime route of colonization of Europe

Peristera Paschou et al.

The Neolithic populations, which colonized Europe approximately 9,000 y ago, presumably migrated from Near East to Anatolia and from there to Central Europe through Thrace and the Balkans. An alternative route would have been island hopping across the Southern European coast. To test this hypothesis, we analyzed genome-wide DNA polymorphisms on populations bordering the Mediterranean coast and from Anatolia and mainland Europe. We observe a striking structure correlating genes with geography around the Mediterranean Sea with characteristic east to west clines of gene flow. Using population network analysis, we also find that the gene flow from Anatolia to Europe was through Dodecanese, Crete, and the Southern European coast, compatible with the hypothesis that a maritime coastal route was mainly used for the migration of Neolithic farmers to Europe.

June 06, 2014

UPDATE:
Two observations: it seems that West/East Eurasian Y chromosomes were sometimes associated with East/West mtDNA and vice versa, so these samples don't appear to be two disjoint West/East Eurasian populations, but some mixing took place. Also, the pigmentation estimates are mainly brown eyes (one blue-eyed individual) and black/dark brown hair (although both brown/dark blond were present).

The STRUCTURE results (which should be interpreted with great caution because of the small number of autosomal loci used) do suggest that this was a population that was more West than East Eurasian autosomally.

Forensic Science International: Genetics Received 2 January 2014; received in revised form 21 May 2014; accepted 25 May 2014. published online 04 June 2014.

Strong genetic admixture in the Altai at the Middle Bronze Age revealed by uniparental and ancestry informative markers

Clémence Hollard et al.

The Altai Mountains have been a long term boundary zone between the Eurasian Steppe populations and South and East Asian populations. To disentangle some of the historical population movements in this area, 14 ancient human specimens excavated in the westernmost part of the Mongolian Altai were studied. Thirteen of them were dated from the Middle to the End of the Bronze Age and one of them to the Eneolithic period. The environmental conditions encountered in this region led to the good preservation of DNA in the human remains. Therefore, a multi-markers approach was adopted for the genetic analysis of identity, ancestry and phenotype markers. Mitochondrial DNA analyses revealed that the ancient Altaians studied carried both Western (H, U, T) and Eastern (A, C, D) Eurasian lineages. In the same way, the patrilineal gene pool revealed the presence of different haplogroups (Q1a2a1-L54, R1a1a1b2-Z93 and C), probably marking different origins for the male paternal lineages. To go further in the search of the origin of these ancient specimens, phenotypical characters (ie: hair and eye colour) were determined. For this purpose, we adapted the HIrisPlex assay recently described to MALDI-TOF mass spectrometry. In addition, some ancestry informative markers were analyzed with this assay. The results revealed mixed phenotypes among this group confirming the probable admixed ancestry of the studied Altaian population at the Middle Bronze Age. The good results obtained from ancient DNA samples suggest that this approach might be relevant for forensic casework too.

Figure on the left shows Fst values between the ancient PPNB population and modern populations.

PLOS Genetics DOI: 10.1371/journal.pgen.1004401

Ancient DNA Analysis of 8000 B.C. Near Eastern Farmers Supports an Early Neolithic Pioneer Maritime Colonization of Mainland Europe through Cyprus and the Aegean Islands

Eva Fernández et al.

The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years. Within this context, ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe. However, the lack of available data from the original Near Eastern farmers has limited the achieved conclusions, preventing the formulation of continental models of Neolithic expansion. Here we address this issue by presenting mitochondrial DNA data of the original Near-Eastern Neolithic communities with the aim of providing the adequate background for the interpretation of Neolithic genetic data from European samples. Sixty-three skeletons from the Pre Pottery Neolithic B (PPNB) sites of Tell Halula, Tell Ramad and Dja'de El Mughara dating between 8,700–6,600 cal. B.C. were analyzed, and 15 validated mitochondrial DNA profiles were recovered. In order to estimate the demographic contribution of the first farmers to both Central European and Western Mediterranean Neolithic cultures, haplotype and haplogroup diversities in the PPNB sample were compared using phylogeographic and population genetic analyses to available ancient DNA data from human remains belonging to the Linearbandkeramik-Alföldi Vonaldiszes Kerámia and Cardial/Epicardial cultures. We also searched for possible signatures of the original Neolithic expansion over the modern Near Eastern and South European genetic pools, and tried to infer possible routes of expansion by comparing the obtained results to a database of 60 modern populations from both regions. Comparisons performed among the 3 ancient datasets allowed us to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain. Moreover, the observed genetic affinities between the PPNB samples and the modern populations of Cyprus and Crete seem to suggest that the Neolithic was first introduced into Europe through pioneer seafaring colonization.

The highly structured distribution of Y-chromosome haplogroups suggests that current patterns of variation may be informative of past population processes. However, limited phylogenetic resolution, particularly of subclades within haplogroup K, has obscured the relationships of lineages that are common across Eurasia. Here we genotype 13 new highly informative single-nucleotide polymorphisms in a worldwide sample of 4413 males that carry the derived allele at M526, and reconstruct an NRY haplogroup tree with significantly higher resolution for the major clade within haplogroup K, K-M526. Although K-M526 was previously characterized by a single polytomy of eight major branches, the phylogenetic structure of haplogroup K-M526 is now resolved into four major subclades (K2a–d). The largest of these subclades, K2b, is divided into two clusters: K2b1 and K2b2. K2b1 combines the previously known haplogroups M, S, K-P60 and K-P79, whereas K2b2 comprises haplogroups P and its subhaplogroups Q and R. Interestingly, the monophyletic group formed by haplogroups R and Q, which make up the majority of paternal lineages in Europe, Central Asia and the Americas, represents the only subclade with K2b that is not geographically restricted to Southeast Asia and Oceania. Estimates of the interval times for the branching events between M9 and P295 point to an initial rapid diversification process of K-M526 that likely occurred in Southeast Asia, with subsequent westward expansions of the ancestors of haplogroups R and Q.

June 01, 2014

Hair color differences are among the most obvious examples of phenotypic variation in humans. Although genome-wide association studies (GWAS) have implicated multiple loci in human pigment variation, the causative base-pair changes are still largely unknown1. Here we dissect a regulatory region of the KITLG gene (encoding KIT ligand) that is significantly associated with common blond hair color in northern Europeans2. Functional tests demonstrate that the region contains a regulatory enhancer that drives expression in developing hair follicles. This enhancer contains a common SNP (rs12821256) that alters a binding site for the lymphoid enhancer-binding factor 1 (LEF1) transcription factor, reducing LEF1 responsiveness and enhancer activity in cultured human keratinocytes. Mice carrying ancestral or derived variants of the human KITLG enhancer exhibit significant differences in hair pigmentation, confirming that altered regulation of an essential growth factor contributes to the classic blond hair phenotype found in northern Europeans.

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